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- PDB-2brh: Structure-based Design of Novel Chk1 Inhibitors: Insights into Hy... -

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Entry
Database: PDB / ID: 2brh
TitleStructure-based Design of Novel Chk1 Inhibitors: Insights into Hydrogen Bonding and Protein-Ligand Affinity
ComponentsSERINE/THREONINE-PROTEIN KINASE CHK1
KeywordsTRANSFERASE / DRUG DESIGN / FURANOPYRIMIDINE / MOLECULAR RECOGNITION / ONCOLOGY / PYRROLOPYRIMIDINE / ATP-BINDING / CELL CYCLE / DNA DAMAGE / KINASE / NUCLEAR PROTEIN / PHOSPHORYLATION / POLYMORPHISM / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage / histone kinase activity (H3-T11 specific) / negative regulation of mitotic nuclear division / regulation of histone H3-K9 acetylation / regulation of mitotic centrosome separation / chromatin-mediated maintenance of transcription / signal transduction involved in G2 DNA damage checkpoint / regulation of double-strand break repair via homologous recombination / DNA damage induced protein phosphorylation / negative regulation of G0 to G1 transition ...regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage / histone kinase activity (H3-T11 specific) / negative regulation of mitotic nuclear division / regulation of histone H3-K9 acetylation / regulation of mitotic centrosome separation / chromatin-mediated maintenance of transcription / signal transduction involved in G2 DNA damage checkpoint / regulation of double-strand break repair via homologous recombination / DNA damage induced protein phosphorylation / negative regulation of G0 to G1 transition / replicative senescence / positive regulation of cell cycle / condensed nuclear chromosome / DNA damage checkpoint / chromatin / cellular response to mechanical stimulus / peptidyl-threonine phosphorylation / kinase activity / regulation of signal transduction by p53 class mediator / DNA replication / intracellular signal transduction / non-specific serine/threonine protein kinase / cell cycle / protein kinase activity / centrosome / intracellular membrane-bounded organelle / DNA repair / apoptotic process / cellular response to DNA damage stimulus / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Serine/threonine-protein kinase, active site / Protein kinase domain / Protein kinase domain / Checkpoint kinase 1, catalytic domain / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Serine/threonine-protein kinase, active site / Protein kinase domain / Protein kinase domain / Checkpoint kinase 1, catalytic domain / Protein kinase, ATP binding site / Protein kinase-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Serine/threonine-protein kinase Chk1
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFoloppe, N. / Fisher, L.M. / Howes, R. / Kierstan, P. / Potter, A. / Robertson, A.G.S. / Surgenor, A.E.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Structure-Based Design of Novel Chk1 Inhibitors: Insights Into Hydrogen Bonding and Protein-Ligand Affinity.
Authors: Foloppe, N. / Fisher, L.M. / Howes, R. / Kierstan, P. / Potter, A. / Robertson, A.G.S. / Surgenor, A.E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE CHK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4932
Polymers34,1481
Non-polymers3451
Water5,405300
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)44.986, 65.733, 58.494
Angle α, β, γ (deg.)90.00, 94.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide SERINE/THREONINE-PROTEIN KINASE CHK1 / CHK1 KINASE


Mass: 34148.148 Da / Num. of mol.: 1 / Fragment: N-TERMINAL KINASE DOMAIN, RESIDUES 1-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC1/CHK1 1-289 C8H / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O14757, EC: 2.7.1.37
#2: Chemical ChemComp-DFW / N-(5,6-DIPHENYLFURO[2,3-D]PYRIMIDIN-4-YL)GLYCINE


Mass: 345.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15N3O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: PARTICIPATES IN THE ARREST OF THE CELL CYCLE WHEN THE DNA IS DAMAGED OR WHEN UNLIGATED ...FUNCTION: PARTICIPATES IN THE ARREST OF THE CELL CYCLE WHEN THE DNA IS DAMAGED OR WHEN UNLIGATED DNA IS PRESENT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 56.6 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9757
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 19953 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.5 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IA8
Resolution: 2.1→58.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.027 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1631 8.4 %RANDOM
Rwork0.176 ---
Obs0.183 17743 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.12 Å2
2--0.33 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 26 300 2416
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0230.0212173
r_bond_other_d0.0020.021962
r_angle_refined_deg2.0731.9732942
r_angle_other_deg1.28934580
r_dihedral_angle_1_deg7.6415255
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_chiral_restr0.1320.2313
r_gen_planes_refined0.0090.022373
r_gen_planes_other0.0050.02432
r_nbd_refined0.2170.2486
r_nbd_other0.2480.22300
r_nbtor_refined
r_nbtor_other0.0920.21301
r_xyhbond_nbd_refined0.2210.2193
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.2340.218
r_symmetry_vdw_other0.2960.255
r_symmetry_hbond_refined0.4330.219
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it1.1381.51282
r_mcbond_other
r_mcangle_it1.99922077
r_mcangle_other
r_scbond_it2.8573891
r_scbond_other
r_scangle_it4.3354.5865
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 117
Rwork0.249 1339

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